Variant report

Variant	rs11239567
Chromosome Location	chr10:46077011-46077012
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:46074816..46082903-chr10:46083299..46090228,15	K562	blood:
2	chr10:46075326..46077121-chr10:46078521..46080983,2	K562	blood:

Variant related genes	Relation type
ENSG00000165406	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10793618	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10793621	0.86[CHB][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1080264	0.92[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11239558	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11239559	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239564	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239565	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239570	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11239577	1.00[CHB][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11239585	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11239587	1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11528544	1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12217545	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12766066	1.00[CHB][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1565096	0.88[EUR][1000 genomes]
rs1565097	0.85[EUR][1000 genomes]
rs1982794	1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1982795	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1994426	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3740107	0.86[EUR][1000 genomes]
rs3824617	0.92[CHB][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4948673	0.85[EUR][1000 genomes]
rs4949003	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7074524	1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7095806	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73289207	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7900810	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7900977	0.91[EUR][1000 genomes]
rs7918454	0.92[CHB][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430166	chr10:45668894-46148794	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv993428	chr10:45742877-46224333	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv895108	chr10:45878908-46224333	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv895109	chr10:45882741-46210665	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv895112	chr10:46012620-46202216	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1041417	chr10:46021181-46088061	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1052233	chr10:46024620-46088061	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv2761592	chr10:46072872-46090202	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11239567	AGAP4	cis	Artery Tibial	GTEx
rs11239567	ZFAND4	cis	Nerve Tibial	GTEx

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:46072600-46086600	Weak transcription	Small Intestine	intestine
2	chr10:46075200-46077600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr10:46075800-46077600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr10:46075800-46078400	Enhancers	HepG2	liver
5	chr10:46076200-46077200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr10:46076200-46077200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr10:46076200-46077600	Flanking Active TSS	K562	blood
8	chr10:46076200-46078200	Flanking Active TSS	GM12878-XiMat	blood
9	chr10:46076400-46077200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr10:46076400-46077200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr10:46076400-46077200	Enhancers	Ovary	ovary
12	chr10:46076400-46077200	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr10:46076400-46077200	Enhancers	HSMM	muscle
14	chr10:46076400-46077200	Enhancers	NHEK	skin
15	chr10:46076400-46077400	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr10:46076400-46077400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr10:46076400-46077800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr10:46076400-46077800	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr10:46076400-46085600	Weak transcription	HSMMtube	muscle
20	chr10:46076600-46077200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr10:46076600-46077400	Enhancers	Fetal Thymus	thymus
22	chr10:46076600-46077400	Enhancers	HMEC	breast
23	chr10:46076600-46077600	Weak transcription	Brain Anterior Caudate	brain
24	chr10:46076600-46077600	Weak transcription	Gastric	stomach
25	chr10:46076600-46077600	Enhancers	Osteobl	bone
26	chr10:46076600-46078000	Enhancers	Fetal Intestine Small	intestine
27	chr10:46076600-46078200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr10:46076600-46078200	Enhancers	Fetal Intestine Large	intestine
29	chr10:46076600-46078200	Enhancers	Stomach Mucosa	stomach
30	chr10:46076600-46078800	Enhancers	Liver	Liver
31	chr10:46076600-46080400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr10:46076800-46077200	Weak transcription	Colon Smooth Muscle	Colon
33	chr10:46076800-46077400	Enhancers	Primary T cells from cord blood	blood
34	chr10:46076800-46077400	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr10:46076800-46077600	Weak transcription	Right Atrium	heart
36	chr10:46076800-46077800	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr10:46076800-46077800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr10:46076800-46077800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr10:46076800-46077800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr10:46076800-46077800	Enhancers	Duodenum Mucosa	Duodenum
41	chr10:46076800-46078000	Enhancers	Primary B cells from cord blood	blood
42	chr10:46076800-46078000	Enhancers	Primary B cells from peripheral blood	blood
43	chr10:46076800-46078000	Enhancers	Primary hematopoietic stem cells	blood
44	chr10:46076800-46078000	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr10:46076800-46078000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr10:46076800-46078000	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr10:46076800-46078000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr10:46076800-46078200	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr10:46076800-46078200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr10:46076800-46078200	Enhancers	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links